Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations

Authors

• Kaitlin Bullard, University of Arkansas, FayettevilleFollow
• Deborah Okyere, University of Arkansas, FayettevilleFollow
• Shelbi j> Foster, University of Arkansas, Fayetteville
• Asmaa Ali Sadoon, University of Arkansas, FayettevilleFollow
• Jiali Li, University of Arkansas, FayettevilleFollow
• Jingyi Chen, University of Arkansas, FayettevilleFollow
• Yong Wang, University of Arkansas, Fayetteville

Document Type

Article

Publication Date

4-26-2025

Keywords

DNA bows, melting curve, FRET, NAMD, VMD

Abstract

Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg2+ ions at different concentrations. The simulations show that Mg2+ ions reduce the fluctuations of DNA strands, enhance base-pairing, and stabilize bent DNA molecules. The computational results are further verified by both melting curve experiments and ensemble FRET measurements, highlighting the mechanical instability and sensitivity of bent DNA molecules.

Comments

Web of Science

MDPI

Citation

Bullard, K.; Okyere, D.; Foster, S.J.; Sadoon, A.A.; Li, J.; Chen, J.; Wang, Y. Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations. Biosensors 2025, 15, 272. https://doi.org/10.3390/bios15050272

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.